General information for g12937.t27
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 26S proteasome non-ATPase regulatory subunit 4.
Parent gene
- The parent gene g12937 is located on chr_1: 27010180..27011251 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g12937 | g12937.t27 | TTS | g12937.t27 | 27009496 | 27009496 |
| chr_1 | g12937 | g12937.t27 | isoform | g12937.t27 | 27009648 | 27011251 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon1 | 27009648 | 27009871 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon2 | 27009934 | 27010018 |
| chr_1 | g12937 | g12937.t27 | cds | g12937.t27.CDS1 | 27010014 | 27010018 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon3 | 27010138 | 27010699 |
| chr_1 | g12937 | g12937.t27 | cds | g12937.t27.CDS2 | 27010138 | 27010699 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon4 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t27 | cds | g12937.t27.CDS3 | 27010752 | 27010866 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon5 | 27010930 | 27011070 |
| chr_1 | g12937 | g12937.t27 | cds | g12937.t27.CDS4 | 27010930 | 27011070 |
| chr_1 | g12937 | g12937.t27 | exon | g12937.t27.exon6 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t27 | cds | g12937.t27.CDS5 | 27011226 | 27011251 |
| chr_1 | g12937 | g12937.t27 | TSS | g12937.t27 | 27011325 | 27011325 |
Sequences
>g12937.t27 Gene=g12937 Length=1153
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTT
TTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCC
AACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGT
CAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGAT
AAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATT
GTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTG
AATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAA
GAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGT
GGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTA
AGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCA
GCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACA
TCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGGTAAAAAGA
CTTCAGTGACGAGGCTATGCCAGATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTT
TGCTATGCAAATGTCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAAAACGTCC
AAAAAAAGACGATACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTACTGATCC
AGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAAT
ACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAG
CGGATCTAAATAA
>g12937.t27 Gene=g12937 Length=282
MVLESTMICLDNSDYQRNGDYLPTRLNAQKDGINLVCLTKLRSNPENNVGLLTMAKTVEV
LATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVD
KAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQ
EALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQA
ASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPVKRLQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12937.t27 | Coils | Coil | Coil | 117 | 137 | - |
| 8 | g12937.t27 | Coils | Coil | Coil | 221 | 244 | - |
| 7 | g12937.t27 | Gene3D | G3DSA:3.40.50.410 | - | 3 | 186 | 4.6E-70 |
| 15 | g12937.t27 | MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 282 | - |
| 14 | g12937.t27 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 239 | - |
| 13 | g12937.t27 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 257 | - |
| 4 | g12937.t27 | PANTHER | PTHR10223:SF7 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 9 | 267 | 9.7E-110 |
| 5 | g12937.t27 | PANTHER | PTHR10223 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 | 9 | 267 | 9.7E-110 |
| 1 | g12937.t27 | Pfam | PF13519 | von Willebrand factor type A domain | 6 | 113 | 1.2E-21 |
| 3 | g12937.t27 | Pfam | PF02809 | Ubiquitin interaction motif | 212 | 227 | 0.0072 |
| 2 | g12937.t27 | Pfam | PF02809 | Ubiquitin interaction motif | 261 | 275 | 0.021 |
| 16 | g12937.t27 | ProSiteProfiles | PS50234 | VWFA domain profile. | 5 | 188 | 9.725 |
| 18 | g12937.t27 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 211 | 230 | 10.732 |
| 17 | g12937.t27 | ProSiteProfiles | PS50330 | Ubiquitin-interacting motif (UIM) domain profile. | 261 | 280 | 8.566 |
| 12 | g12937.t27 | SMART | SM00327 | VWA_4 | 2 | 188 | 1.8E-4 |
| 11 | g12937.t27 | SMART | SM00726 | uim | 211 | 230 | 0.021 |
| 10 | g12937.t27 | SMART | SM00726 | uim | 261 | 280 | 4.4 |
| 6 | g12937.t27 | SUPERFAMILY | SSF53300 | vWA-like | 4 | 177 | 5.99E-31 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K03029 (26S proteasome regulatory subunit N10)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
